The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms
The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms
复制标题
DOI：
10.1371/journal.pone.0231020
复制
发表时间：
2020-04-15
期刊：
影响因子：
3.7
通讯作者：
Zhang, Shouzhou
中科院分区：
文献类型：
--
作者：
Dong, Shanshan;Chen, Lu;Zhang, Shouzhou
有花植物线粒体基因组以其庞大、可变的编码基因组和不稳定的基因组结构而闻名。现有的早期被子植物线粒体基因组在大小、结构和序列等方面表现出极大的遗传多样性，如Amborella mt基因组中HGT的多样性，睡莲mt基因组中大量重复序列的多样性，鹅掌楸mt基因组中保守的基因进化等。然而，目前已知的早期被子植物mt基因组仍然有限，阻碍了我们对被子植物有丝分裂组进化的全面了解。在这里，我们测序和组装木兰线粒体基因组草案。来自木兰科（木兰科）的基因组序列。我们回收了967，100 bp的单个线性线粒体重叠群，平均读段覆盖率为122 x，GC含量为46.6%。该线粒体基因组草图包含丰富的64个基因组，与鹅掌楸和睡莲相似，包括41个蛋白质编码基因，20个tRNA和3个rRNA。20个顺式剪接和5个反式剪接内含子破坏了木兰mt基因组中的10个蛋白质编码基因。重复序列占基因组草图的27%，1,145个重复序列中有17个显示重组证据。木兰属植物的线粒体基因组虽然部分组装，但仍是被子植物中最大的，可能是由于重复序列的扩增、祖先线粒体DNA的保留以及核基因组序列的整合。对来自91种被子植物代表物种的38个保守蛋白质编码基因的串联数据集的线粒体DNA基因组分析支持木兰科植物与单子叶植物和真双子叶植物的姐妹关系，这与质体证据一致。
The mitochondrial genomes of flowering plants are well known for their large size, variable coding-gene set and fluid genome structure. The available mitochondrial genomes of the early angiosperms show extreme genetic diversity in genome size, structure, and sequences, such as rampant HGTs in Amborella mt genome, numerous repeated sequences in Nymphaea mt genome, and conserved gene evolution in Liriodendron mt genome. However, currently available early angiosperm mt genomes are still limited, hampering us from obtaining an overall picture of the mitogenomic evolution in angiosperms. Here we sequenced and assembled the draft mitochondrial genome of Magnolia biondii Pamp. from Magnoliaceae (magnoliids) using Oxford Nanopore sequencing technology. We recovered a single linear mitochondrial contig of 967,100 bp with an average read coverage of 122 x and a GC content of 46.6%. This draft mitochondrial genome contains a rich 64-gene set, similar to those of Liriodendron and Nymphaea, including 41 protein-coding genes, 20 tRNAs, and 3 rRNAs. Twenty cis-spliced and five trans-spliced introns break ten protein-coding genes in the Magnolia mt genome. Repeated sequences account for 27% of the draft genome, with 17 out of the 1,145 repeats showing recombination evidence. Although partially assembled, the approximately 1-Mb mt genome of Magnolia is still among the largest in angiosperms, which is possibly due to the expansion of repeated sequences, retention of ancestral mtDNAs, and the incorporation of nuclear genome sequences. Mitochondrial phylogenomic analysis of the concatenated datasets of 38 conserved protein-coding genes from 91 representatives of angiosperm species supports the sister relationship of magnoliids with monocots and eudicots, which is congruent with plastid evidence.